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193 results for “co-expression”
Double shrinking (DOSH), a regression-based algorithm for gene regulatory network inference from co-expression data
<p>Data for the preprint "Double shrinking (DOSH), a regression-based algorithm for gene regulatory network inference from co-expression data". The preprint is live on ResearchSquare: <a href="http://t.researchsquare.com/track/click/31114617/doi.org?p=eyJzIjoiWVJQQUYtT09mMXFoWnRoMGk0SlpQZTZqWWpJIiwidiI6MSwicCI6IntcInVcIjozMTExNDYxNyxcInZcIjoxLFwidXJsXCI6XCJodHRwczpcXFwvXFxcL2RvaS5vcmdcXFwvMTAuMjEyMDNcXFwvcnMuMy5ycy0yNzM4NjgzXFxcL3YxXCIsXCJpZFwiOlwiZDMzODNjZGNhNWNiNGE2Yjk5NWRkY2UyNmIyODI5NTlcIixcInVybF9pZHNcIjpbXCIzZGQwZTAxMmExMzk4NDhkNTAzYjI4ZTBiZmU1Y2QxMDcxNzhlZTgwXCJdfSJ9">10.21203/rs.3.rs-2738683/v1</a>.</p>
Data from: Dissecting nutrient-related co-expression networks in phosphate starved poplars
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Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events
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Data from: Co-expression of two subtypes of melatonin receptor on rat M1-type intrinsically photosensitive retinal ganglion cells
Intrinsically photosensitive retinal ganglion cells (ipRGCs) are involved in circadian and other non-image forming visual responses. An open question is whether the activity of these neurons may also be under the regulation mediated by the neurohormone melatonin. In the present work, by double-staining immunohistochemical technique, we studied the expression of MT1 and MT2, two known subtypes of mammalian melatonin receptors, in rat ipRGCs. A single subset of retinal ganglion cells labeled by the specific antibody against melanopsin exhibited the morphology typical of M1-type ipRGCs. Immunoreactivity for both MT1 and MT2 receptors was clearly seen in the cytoplasm of all labeled ipRGCs, indicating that these two receptors were co-expressed in each of these neurons. Furthermore, labeling for both the receptors were found in neonatal M1 cells as early as the day of birth. It is therefore highly plausible that retinal melatonin may directly modulate the activity of ipRGCs, thus regulating non-image forming visual functions.
Data from: Determinants and co-expression of anti-predator responses in amphibian tadpoles: a meta-analysis
A wide range of taxa respond to perceived predation risk (PPR) through inducible defenses, and many prey are capable of responding both behaviorally and morphologically to the same risk event. In cases where multiple defenses confer protection by independent means (i.e., they are mechanistically independent) responses will either be co-expressed, or the expression of one defense will limit the capacity (or need) to respond along another axis. Our ability to generate a broad understanding of these patters has been limited, in part, by difficulties in comparing results across studies that employ distinct experimental protocols. Using the extensive literature on tadpole responses to PPR, we conducted a meta-analysis to identify the ecological and experimental determinants of inducible defence expression. We then assessed whether the magnitude of response to PPR along behavioural versus morphological response axes was positively, or negatively, correlated. The most commonly quantified responses to perceived risk in tadpoles included reductions in movement and swimming behaviour, and altered tail morphology. Our analyses reveal that tadpole behavioural responses are strongly influenced by prey family, predator taxon, evolutionary history with the predator (native vs. non-native), amount of prey consumed by the predator, and how perceived risk was manipulated (e.g., presence vs. absence of alarm cues). Tail morphology was similarly influenced by these factors, but also whether the target prey was palatable to predators. Thus, our results identify ecological and experimental features that critically influence the observed effect size in tadpole responses to PPR. A positive correlation between behavioural and morphological responses in studies where both were measured indicates that trait co-specialization is the predominant pattern of defense deployment in larval amphibians. This positive relationship suggests that survival tends to be maximized in tadpoles through equivalent coactivation of multiple independent axes of protection, opposed to maximal expression along any single axis.
Inference of molecular mechanisms of transcriptional regulation from co-expression data
<p>The accompanying data for the article "Inference of molecular mechanisms of transcriptional regulation from co-expression data". The article is now live on Research Square <a href="https://doi.org/10.21203/rs.3.rs-1262163/v1">10.21203/rs.3.rs-1262163/v1</a></p>
Blockade of LAG3 and PD1 leads to co-expression of cytotoxic and exhaustion gene modules in CD8+ T cells to promote antitumor immunity
<p>This is the data necessary to reproduce the figures from "<em>Blockade of LAG3 and PD1 leads to co-expression of cytotoxic and exhaustion gene modules in CD8+ T cells to promote antitumor immunity</em>" by Cillo et al.</p>
Cabozantinib and Erlotinib for Patients With EGFR and c-Met Co-expressing Metastatic Pancreatic Adenocarcinoma
ClinicalTrials.gov study NCT03213626. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns
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Data from: Co-expression of two subtypes of melatonin receptor on rat M1-type intrinsically photosensitive retinal ganglion cells
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Data from: Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus
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Data from: Sex-biased lncRNAs inversely correlate with sex-opposite gene co-expression networks in diversity outbred mouse liver
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Data from: Determinants and co-expression of anti-predator responses in amphibian tadpoles: a meta-analysis
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Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery
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NKT cells co-expressing a GD2-specific chimeric antigen receptor and IL-15 mediate regression of refractory metastatic neuroblastoma
GEO Series GSE154037. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
GEO Series GSE46915. Caulobacter vibrioides. 15 samples. Type: Expression profiling by high throughput sequencing.
RNA seq data examining response to chemical treatment to build the first gene co-expression network of zebrafish
GEO Series GSE171944. Danio rerio. 170 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder
GEO Series GSE142670. Homo sapiens. 52 samples. Type: Expression profiling by high throughput sequencing.
Extensive re-wiring of epithelial-stromal co-expression networks in breast cancer - ER-positive breast cancer validation dataset
GEO Series GSE68744. Homo sapiens. 148 samples. Type: Expression profiling by array.
Genome-wide analysis of RNA binding proteins co-expression with alternative splicing events in mitral valve prolapse
GEO Series GSE229778. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.